How to parse chunk of CSV data with white space line breaks into list of data frames

It's not clear to me if that function was suppose to be used like that. My guess is not. But you can parse the data manually. Create a list, parse out chunks and save it into a list.

xy <- readLines(con = "test.txt")
xy <- xy[-1]  # remove GENERALIZED BORN

xy <- xy[which(xy != "")]
# Start of a break is needed for names and subsetting in a loop.
breaks <- which(grepl("^.*Energy Terms", x = xy))

dfs <- vector(mode = "list", length = length(breaks))
names(dfs) <- xy[breaks]

# Adding one accounts for the Energy Terms line. It's either here
# or in the loop.
chunks <- breaks + 1

for (chunk in seq_along(chunks)) {
  # If we extract the name and use it to subset, the order of the
  # dfs doesn't really matter.
  chk.name <- xy[chunks[chunk] - 1]
  
  from <- chunks[chunk]
  to <- chunks[chunk + 1] - 2
  
  # When working with the last chunk, this sets the end of the text.
  if (is.na(to)) {
    to <- length(xy)
  }
  
  chk <- xy[from:to]

  tmp <- read.table(
    text =  paste(chk, collapse = "\n"), 
    header = TRUE, 
    comment.char = "", 
    sep = ","
    )
  
  dfs[[chk.name]] <- tmp
}

And the result

$`Complex Energy Terms`
  Frame..     BOND ANGLE
1       0 6603.052  7264
2       1 7434.989  7602

$`Receptor Energy Terms`
  Frame..     BOND    ANGLE
1       0 6140.634 5383.124
2       1 6885.297 5653.664

$`Ligand Energy Terms`
  Frame..     BOND    ANGLE
1       0 462.4183 1881.428
2       1 549.6920 1949.048