diff --git a/unimol/unimol/losses/docking_pose.py b/unimol/unimol/losses/docking_pose.py
index e9b87c0..b541f70 100644
--- a/unimol/unimol/losses/docking_pose.py
+++ b/unimol/unimol/losses/docking_pose.py
@@ -1,7 +1,7 @@
 # Copyright (c) DP Technology.
 # This source code is licensed under the MIT license found in the
 # LICENSE file in the root directory of this source tree.
-
+import torch
 import torch.nn.functional as F
 from unicore import metrics
 from unicore.losses import UnicoreLoss, register_loss
@@ -11,6 +11,9 @@
 class DockingPossLoss(UnicoreLoss):
     def __init__(self, task):
         super().__init__(task)
+        self.eos_idx = task.dictionary.eos()
+        self.bos_idx = task.dictionary.bos()
+        self.padding_idx = task.dictionary.pad()
 
     def forward(self, model, sample, reduce=True):
         """Compute the loss for the given sample.
@@ -24,7 +27,8 @@ def forward(self, model, sample, reduce=True):
         cross_distance_predict, holo_distance_predict = net_outputs[0], net_outputs[1]
 
         ### distance loss
-        distance_mask = sample["target"]["distance_target"].ne(0)  # 0 is padding
+        distance_mask = sample["target"]["distance_target"].ne(0)  # 0 for padding, BOS and EOS
+        # 0 is impossible in the cross distance matrix, all the relevant cross distances are kept
         if self.args.dist_threshold > 0:
             distance_mask &= (
                 sample["target"]["distance_target"] < self.args.dist_threshold
@@ -36,9 +40,10 @@ def forward(self, model, sample, reduce=True):
         )
 
         ### holo distance loss
-        holo_distance_mask = sample["target"]["holo_distance_target"].ne(
-            0
-        )  # 0 is padding
+        token_mask = sample["net_input"]["mol_src_tokens"].ne(self.padding_idx) & \
+                     sample["net_input"]["mol_src_tokens"].ne(self.eos_idx) & \
+                     sample["net_input"]["mol_src_tokens"].ne(self.bos_idx)
+        holo_distance_mask = token_mask.unsqueeze(-1) & token_mask.unsqueeze(1)
         holo_distance_predict_train = holo_distance_predict[holo_distance_mask]
         holo_distance_target = sample["target"]["holo_distance_target"][
             holo_distance_mask
diff --git a/unimol/unimol/losses/unimol.py b/unimol/unimol/losses/unimol.py
index f377540..ef58333 100644
--- a/unimol/unimol/losses/unimol.py
+++ b/unimol/unimol/losses/unimol.py
@@ -162,14 +162,18 @@ def cal_dist_loss(self, sample, dist, masked_tokens, target_key, normalize=False
         masked_distance_target = sample[target_key]["distance_target"][
             dist_masked_tokens
         ]
-        non_pad_pos = masked_distance_target > 0
+        # padding distance
+        nb_masked_tokens = dist_masked_tokens.sum(dim=-1)
+        masked_src_tokens = sample["net_input"]["src_tokens"].ne(self.padding_idx)
+        masked_src_tokens_expanded = torch.repeat_interleave(masked_src_tokens, nb_masked_tokens, dim=0)
+        #
         if normalize:
             masked_distance_target = (
                 masked_distance_target.float() - self.dist_mean
             ) / self.dist_std
         masked_dist_loss = F.smooth_l1_loss(
-            masked_distance[non_pad_pos].view(-1).float(),
-            masked_distance_target[non_pad_pos].view(-1),
+            masked_distance[masked_src_tokens_expanded].view(-1).float(),
+            masked_distance_target[masked_src_tokens_expanded].view(-1),
             reduction="mean",
             beta=1.0,
         )
diff --git a/unimol/unimol/models/unimol.py b/unimol/unimol/models/unimol.py
index aa9644b..ae8329c 100644
--- a/unimol/unimol/models/unimol.py
+++ b/unimol/unimol/models/unimol.py
@@ -229,14 +229,18 @@ def get_dist_features(dist, et):
             if self.args.masked_coord_loss > 0:
                 coords_emb = src_coord
                 if padding_mask is not None:
-                    atom_num = (torch.sum(1 - padding_mask.type_as(x), dim=1) - 1).view(
+                    atom_num = torch.sum(1 - padding_mask.type_as(x), dim=1).view(
                         -1, 1, 1, 1
-                    )
+                    )  # consider BOS and EOS as part of the object
                 else:
-                    atom_num = src_coord.shape[1] - 1
+                    atom_num = src_coord.shape[1]
                 delta_pos = coords_emb.unsqueeze(1) - coords_emb.unsqueeze(2)
                 attn_probs = self.pair2coord_proj(delta_encoder_pair_rep)
                 coord_update = delta_pos / atom_num * attn_probs
+                # Mask padding
+                pair_coords_mask = (1 - padding_mask.float()).unsqueeze(-1) * (1 - padding_mask.float()).unsqueeze(1)
+                coord_update = coord_update * pair_coords_mask.unsqueeze(-1)
+                #
                 coord_update = torch.sum(coord_update, dim=2)
                 encoder_coord = coords_emb + coord_update
             if self.args.masked_dist_loss > 0:
diff --git a/unimol/unimol/utils/docking_utils.py b/unimol/unimol/utils/docking_utils.py
index cc63a8c..af3b31b 100644
--- a/unimol/unimol/utils/docking_utils.py
+++ b/unimol/unimol/utils/docking_utils.py
@@ -180,6 +180,9 @@ def docking_data_pre(raw_data_path, predict_path):
             pocket_coords = pocket_coords.numpy().astype(np.float32)
             distance_predict = distance_predict.numpy().astype(np.float32)
             holo_distance_predict = holo_distance_predict.numpy().astype(np.float32)
+            # Fill diagonal with 0, issue with the model not learning to predict 0 distance
+            holo_distance_predict = np.fill_diagonal(holo_distance_predict, 0)
+            #
             holo_coords = holo_coordinates.numpy().astype(np.float32)
 
             pocket_coords_list.append(pocket_coords)